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Outline

Title
Abstract
Aims and Objectives
Review of Human Mobility Models
Descriptive Analysis of Census Data
Technical Background on GLM and GLMM
Making Inference on the Data and Model Selection
Data on Rural Mobility
Techniques for Addressing Missing Data
Application of Missing Data Techniques
Application on the Abc Data
Data and Preparation
Method
Results
Combining Multiple Data Sources
Objectives
Application on the Data Sets
Fitting a Linear Model for the Combined Data Set
Evaluation of the Method
Conclusion and Discussion
Key Findings
Limitations
Future Work
Conclusion
Introduction
Methods
Study Design and Sample
Discussion
References
All Topics
Mathematics
Statistics

Human Mobility Models with Imperfect Data

Profile image of Thiripura VinoThiripura Vino

2020

https://doi.org/10.7717/PEERJ.3958
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172 pages

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Abstract

Human mobility plays a major role in the spread of communicable diseases. Remote Indigenous populations in Australia tend to have a higher risk of communicable diseases, and although high levels of mobility at the household, community and regional scale are prevalent in these communities, limited data are available on the movement patterns of these populations. This project is motivated by the need to understand and model human mobility in rural regions when hampered by imperfect data, and aims to develop a robust methodology with techniques incorporated to address missing data and integrate multiple sources of data. In this study, I introduce numerous innovations to shed light on imperfect movement data. I applied Generalised Linear Mixed E↵ects Modelling (GLMM) for longitudinal data to understand the long-and medium-term mobility in Indigenous communities. I used Multiple Imputation by Chained Equations (MICE) to address the missing data and Two Sample Two Stage Least Squares (TSTSLS) estimation to combine two data sets with di↵erent variables. The significance of this project is that it creates new knowledge for modelling human mobility with longitudinal data and making inferences based on imperfect data from multiple sources. This knowledge could be e↵ectively used to understand human mobility which could be applied in real world situations such as infectious disease surveillance and control. vii Acknowledgements I first thank my principal supervisor Prof. Andrew Robinson and my cosupervisors Dr. Nic Geard and Dr. Trish Campbell. Your guidance, constructive feedback, support and your encouragement were invaluable in completing this journey. Thank you very much for giving me the opportunity to work with you, your time and encouragement to work independently to solve the challenges and expand my skills throughout the project.

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    Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection
    Rebecca Chisholm

    Group A Streptococcus (GAS) skin infections are caused by a diverse array of strain types and are highly prevalent in Indigenous and other disadvantaged populations. The role of strain-specific immunity in preventing GAS infections is poorly understood, representing a critical knowledge gap in vaccine development. A recent GAS murine challenge study showed evidence that sterilising strain-specific and enduring immunity required two skin infections by the same GAS strain within three weeks. This mechanism of developing enduring immunity may be a significant impediment to the accumulation of immunity in populations.We used a mathematical model of GAS transmission to investigate the epidemiological consequences of enduring strain-specific immunity developing only after two infections with the same strain within a specified interval. Accounting for uncertainty when correlating murine timeframes to humans, we varied this maximum inter-infection interval from 3 to 420 weeks to assess its ...

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    Modelling testing and response strategies for COVID-19 outbreaks in remote Australian Aboriginal communities
    Rebecca Chisholm

    BMC Infectious Diseases

    Background Remote Australian Aboriginal and Torres Strait Islander communities have potential to be severely impacted by COVID-19, with multiple factors predisposing to increased transmission and disease severity. Our modelling aims to inform optimal public health responses. Methods An individual-based simulation model represented SARS-CoV2 transmission in communities ranging from 100 to 3500 people, comprised of large, interconnected households. A range of strategies for case finding, quarantining of contacts, testing, and lockdown were examined, following the silent introduction of a case. Results Multiple secondary infections are likely present by the time the first case is identified. Quarantine of close contacts, defined by extended household membership, can reduce peak infection prevalence from 60 to 70% to around 10%, but subsequent waves may occur when community mixing resumes. Exit testing significantly reduces ongoing transmission. Concurrent lockdown of non-quarantined ho...

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    Formative evaluation of a community‐based approach to reduce the incidence of Strep A infections and acute rheumatic fever
    Ayu masyeni

    Australian and New Zealand Journal of Public Health, 2021

    Objectives: To explore the acceptability of a novel, outreached-based approach to improve primary and primordial prevention of Strep A skin sores, sore throats and acute rheumatic fever in remote Aboriginal communities. A comprehensive prevention program delivered by trained Aboriginal Community Workers was evaluated using approximately fortnightly household surveys about health and housing and clinical records. Results: Twenty-seven primary participants from three remote Aboriginal communities in the Northern Territory consented, providing 37.8 years of retrospective baseline data and 18.5 years of prospective data during the study period. Household members were considered to be secondary participants. Five Aboriginal Community Workers were trained and employed, delivering a range of supports to households affected by acute rheumatic fever including environmental health support and education. Clinical record audit and household self-report of Strep A infections were compared. No association between clinical-and self-report was identified. Ongoing participation suggests this outreach-based prevention program was acceptable and associated with improved reporting of household maintenance issues and awareness of prevention opportunities for Strep A infections. Implications for public health: Biomedical, clinic-based approaches to the management of Strep A infections in remote communities can be usefully augmented by outreach-based supports delivered by Aboriginal Community Workers responding to community needs.

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    Quantifying heterogeneous contact patterns in Japan: a social contact survey
    Lankeshwara Munasinghe

    Theoretical Biology and Medical Modelling, 2019

    Background: Social contact surveys can greatly help in quantifying the heterogeneous patterns of infectious disease transmission. The present study aimed to conduct a contact survey in Japan, offering estimates of contact by age and location and validating a social contact matrix using a seroepidemiological dataset of influenza. Methods: An internet-based questionnaire survey was conducted, covering all 47 prefectures in Japan and including a total of 1476 households. The social contact matrix was quantified assuming reciprocity and using the maximum likelihood method. By imposing several parametric assumptions for the next-generation matrix, the empirical seroepidemiological data of influenza A (H1N1) 2009 was analysed and we estimated the basic reproduction number, R 0. Results: In total, the reported number of contacts on weekdays was 10,682 whereas that on weekend days was 8867. Strong age-dependent assortativity was identified. Forty percent of weekday contacts took place at schools or workplaces, but that declined to 14% on weekends. Accounting for the age-dependent heterogeneity with the known social contact matrix, the minimum value of the Akaike information criterion was obtained and R 0 was estimated at 1.45 (95% confidence interval: 1.42, 1.49). Conclusions: Survey datasets will be useful for parameterizing the heterogeneous transmission model of various directly transmitted infectious diseases in Japan. Age-dependent assortativity, especially among children, along with numerous contacts in school settings on weekdays implies the potential effectiveness of school closure.

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    Levels of pneumococcal conjugate vaccine coverage and indirect protection against invasive pneumococcal disease and pneumonia hospitalisations in Australia: An observational study
    Sanjay Jayasinghe

    PLOS Medicine, 2021

    There is limited empiric evidence on the coverage of pneumococcal conjugate vaccines (PCVs) required to generate substantial indirect protection. We investigate the association between population PCV coverage and indirect protection against invasive pneumococcal disease (IPD) and pneumonia hospitalisations among undervaccinated Australian children. Birth and vaccination records, IPD notifications, and hospitalisations were individually linked for children aged <5 years, born between 2001 and 2012 in 2 Australian states (New South Wales and Western Australia; 1.37 million children). Using Poisson regression models, we examined the association between PCV coverage, in small geographical units, and the incidence of (1) 7-valent PCV (PCV7)-type IPD; (2) all-cause pneumonia; and (3) pneumococcal and lobar pneumonia hospitalisation in undervaccinated children. Undervaccinated children received <2 doses of PCV at <12 months of age and no doses at �12 months of age. Potential confounding variables were selected for adjustment a priori with the assistance of a directed acyclic graph.

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